A tag is a keyword or label that categorizes your question with other, similar questions. Using the right tags makes it easier for others to find and answer your question.
Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackex…
if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design…
python is a programming language, widely used in bioinformatics
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
to refer to the alignment of nucleotide or peptide sequences, producing an arrangement that maximizes similarity between sequences.
use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific …
for questions related to single-cell RNA-seq.
Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees
To be used for questions specific tothe sequence file format `.fasta`. Please minimise usage if the question is more generally about sequence formats.
for questions specifically related to the text SAM format. For general questions about the SAM/BAM formats use the tag BAM.
VCF, acronym for Variant Calling Format, is a text file type used to store information regarding genetic variants.
Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.
Seurat is a package for analyzing single cell rna seq data.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
to refer to the gene sequence/coding part of the sequence.
The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.
Single Nucleotide Polymorphisms. How to find them? How to correlate them with other data? How to represent them? What is their distribution?
Questions about techniques in which the genetic material of a single cell is analysed individually
Umbrella term for understanding any given nucleic acid sequence code, either as a locus, loci or genome with itself or as a comparison to comparable nucleic acid sequence code either intraspecificall…
A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.
Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or tr…
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
Genomics is an interdisciplinary field of science focusing on the structure, function, evolution, mapping, and editing of genomes.
Use it when comparing a measure of the expression between two (or more) samples, where the units are relative to the comparison.
A file format used in structural biology to describe the 3-D coordinates of atoms of a biological structure, often a protein. Can also refer to the Protein Data Bank database, which stores all the sub…
Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.
Deseq2 is an R package for analyzing RNA sequencing data
FASTQ is a file format use to store short reads and their quality values
The process of discovering variants in individuals starting from sequencing reads. Can be subdivided into germline variant calling and somatic variant calling. Can also be used for the more specific p…
for questions about how to use, download, retrieve, check and browse public databases.
to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell). It has notable programmatic strengths over C shell (csh) and touch C shell (tcsh)